Variant report

Variant	rs62250272
Chromosome Location	chr3:28489463-28489464
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:28388988..28390557-chr3:28488307..28491237,2	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-CMC1-4	chr3:28489216-28489564	NONHSAT088791

Variant related genes	Relation type
ENSG00000163512	Chromatin interaction

Extended variants
information (count: 101 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:94)

rs_ID	r²[population]
rs1037723	0.84[AMR][1000 genomes];0.80[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11705962	0.93[ASN][1000 genomes]
rs11706332	0.86[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs11707705	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11710963	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11712484	0.84[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs11712489	0.84[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs11720107	0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11918050	0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11921692	0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11924173	0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11926399	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13066118	0.81[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs13074633	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13075840	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13080155	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13081520	0.87[AMR][1000 genomes];0.82[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13081787	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13087143	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13087774	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13088574	0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13090439	0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13095628	0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13099152	0.82[ASN][1000 genomes]
rs1457909	0.84[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs1457910	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1585211	0.80[ASN][1000 genomes]
rs1606386	0.84[ASN][1000 genomes]
rs17021402	0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17357206	0.87[AMR][1000 genomes];0.80[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs17638742	0.82[ASN][1000 genomes]
rs17638782	0.82[ASN][1000 genomes]
rs17638991	0.84[ASN][1000 genomes]
rs17639978	0.96[EUR][1000 genomes]
rs17695765	0.87[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs17695884	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs17696025	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs17696459	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17696561	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17696783	0.83[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs2018136	0.80[ASN][1000 genomes]
rs2168799	0.80[ASN][1000 genomes]
rs34311197	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs34574968	0.81[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs34796684	0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs35088087	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs35137555	0.84[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs35177150	0.87[AMR][1000 genomes];0.80[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs35702956	0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs35736614	0.82[ASN][1000 genomes]
rs35825908	0.84[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs35845822	0.82[ASN][1000 genomes]
rs36051688	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs36105900	0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3762797	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4234337	0.92[ASN][1000 genomes]
rs4256085	0.92[ASN][1000 genomes]
rs4295137	0.92[ASN][1000 genomes]
rs4322963	0.92[ASN][1000 genomes]
rs4428136	0.91[ASN][1000 genomes]
rs4450765	0.92[ASN][1000 genomes]
rs4452283	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4522735	0.82[ASN][1000 genomes]
rs4680753	0.92[ASN][1000 genomes]
rs58918848	0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs59975750	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs60043893	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs62250271	0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62250273	0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs62250296	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62251105	0.84[ASN][1000 genomes]
rs62251108	0.82[ASN][1000 genomes]
rs62251131	0.93[ASN][1000 genomes]
rs62251134	0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs62251138	0.85[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs62251144	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs62252069	0.82[ASN][1000 genomes]
rs6551255	0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs66733194	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs66767946	0.87[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs6771460	0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs68085718	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs71087683	0.82[ASN][1000 genomes]
rs7434193	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7627471	0.91[ASN][1000 genomes]
rs7627575	0.92[ASN][1000 genomes]
rs7635383	0.84[ASN][1000 genomes]
rs7638450	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7643191	0.84[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs7650831	0.81[ASN][1000 genomes]
rs952888	0.82[ASN][1000 genomes]
rs9683360	0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs969443	0.87[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs9817953	0.81[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3328565	chr3:27991169-28915035	Weak transcription Enhancers Active TSS ZNF genes & repeats Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
2	nsv876649	chr3:28126595-28718454	Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Weak transcription Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
3	nsv876650	chr3:28427029-28613602	Enhancers Weak transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
4	nsv1015015	chr3:28461972-28728494	Bivalent/Poised TSS Active TSS Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
5	nsv916364	chr3:28468275-29146280	Enhancers Bivalent Enhancer Weak transcription ZNF genes & repeats Bivalent/Poised TSS Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
6	nsv590010	chr3:28469830-28727214	Enhancers Active TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
7	nsv979813	chr3:28478897-28489553	Weak transcription Strong transcription ZNF genes & repeats	TF binding region Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:5 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:28473200-28492400	Weak transcription	Gastric	stomach
2	chr3:28479800-28509000	Weak transcription	Left Ventricle	heart
3	chr3:28483600-28497000	Weak transcription	Brain Substantia Nigra	brain
4	chr3:28483800-28497600	Weak transcription	Ovary	ovary
5	chr3:28489400-28490000	Weak transcription	Skeletal Muscle Male	skeletal muscle

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